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- PDB-4dbz: Crystal Structure of V151L Actinorhodin Polyketide Ketoreductase ... -

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Basic information

Entry
Database: PDB / ID: 4dbz
TitleCrystal Structure of V151L Actinorhodin Polyketide Ketoreductase with NADPH
ComponentsKetoacyl reductase
KeywordsOXIDOREDUCTASE / Rossmann fold / ketoreductase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / steroid metabolic process / antibiotic biosynthetic process / oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Putative ketoacyl reductase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.643 Å
AuthorsJavidpour, P. / Tsai, S.-C.
CitationJournal: Chem.Biol. / Year: 2013
Title: The Determinants of Activity and Specificity in Actinorhodin Type II Polyketide Ketoreductase.
Authors: Javidpour, P. / Bruegger, J. / Srithahan, S. / Korman, T.P. / Crump, M.P. / Crosby, J. / Burkart, M.D. / Tsai, S.C.
History
DepositionJan 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketoacyl reductase
B: Ketoacyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4484
Polymers58,9572
Non-polymers1,4912
Water79344
1
A: Ketoacyl reductase
B: Ketoacyl reductase
hetero molecules

A: Ketoacyl reductase
B: Ketoacyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8958
Polymers117,9144
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16980 Å2
ΔGint-84 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.934, 102.934, 121.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ketoacyl reductase


Mass: 29478.389 Da / Num. of mol.: 2 / Mutation: V151L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: actIII, SCBAC28G1.12c, SCO5086 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P16544, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Tris-Cl, 1.8 M Na malonate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 21581

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Processing

Software
NameVersionClassification
CCP4model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.643→47.4185 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 1097 5.08 %
Rwork0.1788 --
obs0.1807 21581 96.52 %
all-22389 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.308 Å2 / ksol: 0.401 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6734 Å20 Å2-0 Å2
2--5.6734 Å2-0 Å2
3----11.3468 Å2
Refinement stepCycle: LAST / Resolution: 2.643→47.4185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 96 44 3939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083955
X-RAY DIFFRACTIONf_angle_d1.1325389
X-RAY DIFFRACTIONf_dihedral_angle_d19.0721417
X-RAY DIFFRACTIONf_chiral_restr0.067637
X-RAY DIFFRACTIONf_plane_restr0.004693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.643-2.76310.2611180.19812353X-RAY DIFFRACTION90
2.7631-2.90880.27591270.19382430X-RAY DIFFRACTION93
2.9088-3.0910.22561310.20042479X-RAY DIFFRACTION95
3.091-3.32960.24781250.18772559X-RAY DIFFRACTION96
3.3296-3.66460.2141580.1762560X-RAY DIFFRACTION98
3.6646-4.19450.23141670.1682632X-RAY DIFFRACTION100
4.1945-5.28360.17831370.16452668X-RAY DIFFRACTION100
5.2836-47.41850.21081340.1842803X-RAY DIFFRACTION100

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